Felix Gaeta is Absolutely, Positively a Cylon
Ok so I have been promising this for a very long time, and I keep putting it off, and so I have forgotten some of my evidence. But believe me! and I will update this as I remember/rewatch the episodes. Also let me note that I have only watched up through episode 2.5 (The Farm), so please don't spoiler anything that comes after that. Ok? Ok!
1. The first piece of evidence is more a logistics issue than anything. The Cylons are obviously very good at this infiltration business; they know exactly where they ought to have particular agents in order to achieve the maximum effect with the invasion, in terms of both emotional stimuli and logistical considerations. By emotional stimuli I mean that they know to send extremely hot, sex-crazed Six for Gaius Baltar, who responds quickly to that combination; cute and smiley Sharon ought to be the one seducing Helo down on Caprica, rather than Six, who's kind of cold and a little crazy when you get right down to it; and Simon, who gives off a warmth to him, is better suited to try to coax Starbuck into staying at the hospital than Leoben or Aaron Doral would be.
And by logistics I mean the obvious: WHY IS THERE ONLY ONE CYLON IN THE COLONIAL FLEET? The Cylons are not stupid. Sharon has access to some stuff, but she's only a Raptor pilot. She has no way of getting to the inner workings of the fleet besides putting her cover at risk (ie. sneaking away to blow up the water tanks). What the Cylons would ideally have is someone who can affect the fleet without ever being noticed - "oops! Hey, we've been boarded!" and such. Gaeta is in the ideal position for that, obviously.
Which leads me to my plot-based evidence.
2. Magical Cylon spy device!
Appears in CIC! And straight-edge, conscientious, hyper-affirmation-seeking Gaeta's response? "Wait, uh, didn't you put that there?" WRONG. This is totally out of character for the kid. Gaeta has his business together (mostly) and seeing Aaron Doral creeping around CIC installing an iSpy would make him freak out. Unless he wasn't there on purpose - or didn't see on purpose - or installed it himself.
3. "I studied bioinformatics before I signed up for the Colonial fleet."
What is a Cylon?
Biological parts +
HUH. HOW ABOUT THAT.
4. Cylon detector.
Adama asks Gaeta to help on the Cylon detector. Do we ever see him do that? In fact, do we ever see him have anything at all to do with the entire detection process, other than letting drop the previous tidbit and not-bragging-really around the poker table? This could be because of Baltar and his total not-knowing-anything, which would be fine, but it seems very off for Gaeta, especially given his "give me more work, sir!" tendencies. Wouldn't you expect him to be all up in Baltar's grill or something?
5. Infamous hand movement.
Right before Sharon shoots Adama, the camera pans down to focus on her left arm meeting Gaeta's right. You don't see anything pass between them, and it's unlikely that he's handing her a sidearm - she has her own - but then we don't know how Sharon is triggered to shoot Adama (it's not conscious, as we can tell by the soundtrack that she's pretty much in a phased state when in happens). Does Gaeta have secret triggery Cylon pheromones, and when he shakes her hand they go poof? I don't know. I don't consider this definitive proof of anything, but it is, er, curious.
6. The entire world explodes after Adama gets shot.
The Cylons are bearing in and the fleet needs to jump. Ok. Who messes up the jump coordinates? Who comes up with a solution that involves networking the computers, the sole way the Cylons can gain comprehensive access to the ship's systems? Who writes the (FAILED) firewalls to try to keep the Cylons out? BING BING! Gaeta. All of these things allow the Cylons to infiltrate the Vipers' perimeter, board the Galactica, and get a bullet's-width away from venting the entire crew of the Galactica into space. Pretty good invasion tactic, especially if you have an inside man messing things up on purpose for you.
7. "I reran the security protocol".
In the episode where the corporeal Six tries to accuse Baltar of treason with the faked photo (Season One, Episode somethin or other), it's looking like Baltar's going to be convicted because everyone believes the photo is of him. The only thing that saves him is Six towering over him, telling him to repent, which he does at the last possible second. Coincidentally, as soon as Baltar repents, the photo is discovered to be a fake. By Gaeta. Who just, mmm, miraculously happened to rerun the security sweep on the photo, like, the SECOND after Baltar gets on his knees and whines to Six. HOW ABOUT THAT?!
8. Silly details.
I just saw this tonight as I was rewatching Colonial Day. During the last scene - the ballroom dance - the producers have everyone ticked off into their respective couples. Lee/Starbuck/Baltar have this weird menage a trois going, Laura dances with Adama, Dee and Billy are rocking out in a corner - and a red-befrocked Sharon is twirling on the arm of our good friend Felix Gaeta. Why would these kids even GO together? There's really been no proof they even know or like each other - they never communicate in any way. Except, of course, if they're both Cylons, in which case they match right up. Hrrrm.
I reserve the right to update this list! because I am a dooooork.